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PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

Huaiyu Mi, Qing Dong, Anushya Muruganujan, Pascale Gaudet, Suzanna Lewis, Paul D. Thomas
2009 Nucleic Acids Research  
Collaboration with GO Consortium For almost 2 years now, there has been a formal collaboration between the Gene Ontology Consortium and the PANTHER database (5) .  ...  For PANTHER 7 trees, complete protein-coding gene sets for 48 different organisms were carefully constructed from a number of different sources, in collaboration with the GO Consortium, with an effort  ... 
doi:10.1093/nar/gkp1019 pmid:20015972 pmcid:PMC2808919 fatcat:lbejzfgrlvapznianbogbiosjy

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

Huaiyu Mi, Anushya Muruganujan, Dustin Ebert, Xiaosong Huang, Paul D Thomas
2018 Nucleic Acids Research  
For evolutionary classifications, we have added more prokaryotic and plant genomes to the phylogenetic gene trees, expanding the representation of gene evolution in these lineages.  ...  PANTHER (Protein Analysis Through Evolutionary Relationships, http://pantherdb.org) is a resource for the evolutionary and functional classification of genes from organisms across the tree of life.  ...  Improved family boundaries The PANTHER team has been collaborating with the Ensembl Compara/TreeFam (18) boundaries for inferring phylogenetic trees.  ... 
doi:10.1093/nar/gky1038 pmid:30407594 fatcat:cz662zk7yjhbrn2ph6l75ckdq4

PANTHER version 10: expanded protein families and functions, and analysis tools

Huaiyu Mi, Sagar Poudel, Anushya Muruganujan, John T. Casagrande, Paul D. Thomas
2015 Nucleic Acids Research  
The latest version of PANTHER, 10.0, includes almost 5000 new protein families (for a total of over 12 000 families), each with a reference phylogenetic tree including protein-coding genes from 104 fully  ...  Phylogenetic trees now include inference of horizontal transfer events in addition to speciation and gene duplication events.  ...  ACKNOWLEDGEMENT The authors want to acknowledge the contributions of the GO Phylogenetic Annotation curators: Marc Feuermann, Pascale Gaudet, Karen Christie, Donghui Li.  ... 
doi:10.1093/nar/gkv1194 pmid:26578592 pmcid:PMC4702852 fatcat:2ibdraz7s5ak3hbtvfzujlyiry

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API

Huaiyu Mi, Dustin Ebert, Anushya Muruganujan, Caitlin Mills, Laurent-Philippe Albou, Tremayne Mushayamaha, Paul D Thomas
2020 Nucleic Acids Research  
The evolutionary classification is based on a library of over 15,000 phylogenetic trees, and the functional classifications include Gene Ontology terms and pathways.  ...  We have added human enhancer-gene links that associate non-coding regions with the annotated human genes in PANTHER.  ...  ACKNOWLEDGEMENTS The authors want to thank the GO Phylogenetic Annotation curators for QA of the phylogenetic trees and family members: Marc Feuermann, Michael Kesling, Pascale Gaudet, Karen Christie,  ... 
doi:10.1093/nar/gkaa1106 pmid:33290554 pmcid:PMC7778891 fatcat:ud5tcejh2fgifjkxjwoz7rc6aq

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

Huaiyu Mi, Anushya Muruganujan, Paul D. Thomas
2012 Nucleic Acids Research  
The main goals of PANTHER remain essentially unchanged: the accurate inference (and practical application) of gene and protein function over large sequence databases, using phylogenetic trees to extrapolate  ...  The data and tools in PANTHER-a comprehensive, curated database of protein families, trees, subfamilies and functions available at http:// pantherdb.org-have undergone continual, extensive improvement  ...  ACKNOWLEDGEMENTS We thank John Casagrande for PANTHER database extensions and data loader enhancements in version 8. Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gks1118 pmid:23193289 pmcid:PMC3531194 fatcat:penzalro4zfajejys6bs2cas5u

Sensing the cilium, digital capture of ciliary data for comparative genomics investigations

Karen R. Christie, Judith A. Blake
2018 Cilia  
In addition, ciliary terminology in the GO itself was improved in collaboration with GO ontology developers and the SYSCILIA Consortium.  ...  We worked closely with the GO Consortium ontology development editors and the SYSCILIA Consortium to improve the representation of ciliary biology within the GO.  ...  Acknowledgements We thank Joel Richardson and Mary Dolan at Mouse Genome Informatics for helpful discussions regarding interpretation of the VLAD enrichment results.  ... 
doi:10.1186/s13630-018-0057-0 pmid:29713460 pmcid:PMC5907423 fatcat:fw6aagqp5zccjartsvkv2tel6i

The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species

Philip E. Bourne
2009 PLoS Computational Biology  
The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic  ...  way and in a species-neutral manner with the aim of unifying the representation of gene function across different organisms.  ...  Author Contributions Conceived and designed the experiments: The Reference Genome Group of the Gene Ontology Consortium. Analyzed the data: The Reference Genome Group of the Gene Ontology Consortium.  ... 
doi:10.1371/journal.pcbi.1000431 pmid:19578431 pmcid:PMC2699109 fatcat:blqwavhitja55gglige46ch7sm

Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium

P. Gaudet, M. S. Livstone, S. E. Lewis, P. D. Thomas
2011 Briefings in Bioinformatics  
The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data.  ...  Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are  ...  The curator verifies that the PANTHER tree topology is consistent with those orthologous clusters, and with any published phylogenetic analyses.  ... 
doi:10.1093/bib/bbr042 pmid:21873635 pmcid:PMC3178059 fatcat:xiylkiwb6bdktchiy7sasi5nuy

The Gene Ontology's Reference Genome Project: *A Unified Framework for Functional Annotation across Species

Pascale Gaudet, Pascale Gaudet, Reference Genome Group
2009 Nature Precedings  
The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in a highly systematic  ...  way and in a species-neutral manner with the aim of unifying the representation of gene function across different organisms.  ...  Author Contributions Conceived and designed the experiments: The Reference Genome Group of the Gene Ontology Consortium. Analyzed the data: The Reference Genome Group of the Gene Ontology Consortium.  ... 
doi:10.1038/npre.2009.3150 fatcat:yuj2nxyoqjfhnltwlhzu2wobmm

The Gene Ontology resource: enriching a GOld mine

Gene Ontology Consortium
2020 Nucleic Acids Research  
The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products.  ...  The new GO-CAM annotation framework was notably improved, and we formalized the model with a computational schema to check and validate the rapidly increasing repository of 2838 GO-CAMs.  ...  ACKNOWLEDGEMENTS We want to thank all the contributors to the GO resource over the last 20 years (http://geneontology.org/ page/acknowledgments-contributors), and all the authors  ... 
doi:10.1093/nar/gkaa1113 pmid:33290552 pmcid:PMC7779012 fatcat:socxl3x5svamfoc2sobzyvjjoy

Alliance of Genome Resources Portal: unified model organism research platform

2019 Nucleic Acids Research  
The Alliance of Genome Resources (Alliance) is a consortium of the major model organism databases and the Gene Ontology that is guided by the vision of facilitating exploration of related genes in human  ...  Initiated in 2016, the Alliance is building a central portal (www.alliancegenome.org) for access to data for the primary model organisms along with gene ontology data and human data.  ...  ACKNOWLEDGEMENTS The Alliance platform is designed and implemented by a core group of developers and curators at SGD, Worm-Base, ZFIN, RGD, MGD, FlyBase and the GOC.  ... 
doi:10.1093/nar/gkz813 pmid:31552413 pmcid:PMC6943066 fatcat:kfgyjj7jybclndvfjbk5s53wci

Ensembl 2017

Bronwen L. Aken, Premanand Achuthan, Wasiu Akanni, M. Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Laurent Gil, Carlos García Girón (+38 others)
2016 Nucleic Acids Research  
Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees.  ...  Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites.  ...  ACKNOWLEDGEMENTS Thank you to the Systems Administration teams at the Wellcome Trust Sanger Institute and at EMBL-EBI for  ... 
doi:10.1093/nar/gkw1104 pmid:27899575 pmcid:PMC5210575 fatcat:hzc4nlutrnfo5obbhqtlljr724

Ensembl Genomes 2020-enabling non-vertebrate genomic research

2019 Nucleic Acids Research  
the tree of life.  ...  These include the continued growth, more robust and reproducible sets of orthologues and paralogues, and enriched views of gene expression and gene function in plants.  ...  ACKNOWLEDGEMENTS We would like to acknowledge the following Ensembl developers for developing and maintaining the front-end and back-end software and infrastructure that underpins Ensembl Genomes: Premanand  ... 
doi:10.1093/nar/gkz890 pmid:31598706 pmcid:PMC6943047 fatcat:vj27adwlbnbq3hzxxei5nj55ji

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

Marcela K Tello-Ruiz, Sushma Naithani, Parul Gupta, Andrew Olson, Sharon Wei, Justin Preece, Yinping Jiao, Bo Wang, Kapeel Chougule, Priyanka Garg, Justin Elser, Sunita Kumari (+17 others)
2020 Nucleic Acids Research  
The current release, #63 (October 2020), hosts 93 reference genomes—over 3.9 million genes in 122 947 families with orthologous and paralogous classifications.  ...  We train plant researchers in biocuration of genes and pathways; host curated maize gene structures as tracks in the maize genome browser; and integrate curated rice genes and pathways in the Plant Reactome  ...  Marco and David Micklos (MaizeCode Project) for jointly running the maize gene structural annotation jamborees.  ... 
doi:10.1093/nar/gkaa979 pmid:33170273 fatcat:atundz637bfalivwtye3vb3twe

EcoliWiki: a wiki-based community resource for Escherichia coli

Brenley K. McIntosh, Daniel P. Renfro, Gwendowlyn S. Knapp, Chanchala R. Lairikyengbam, Nathan M. Liles, Lili Niu, Amanda M. Supak, Anand Venkatraman, Adrienne E. Zweifel, Deborah A. Siegele, James C. Hu
2011 Nucleic Acids Research  
EcoliWiki integrates the Mediawiki wiki platform with other open-source software tools and in-house software development to extend how wikis can be used for model organism databases.  ...  EcoliWiki content currently covers genes from five laboratory E. coli strains, 21 bacteriophage genomes, F plasmid and eight transposons.  ...  Peter Karp generously helped us use EcoCyc to seed EcoliWiki with content about E. coli genes.  ... 
doi:10.1093/nar/gkr880 pmid:22064863 pmcid:PMC3245172 fatcat:uznhoukfjbc2lhthu6iiekhipm
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